Gene Expression in Nitrogen-Fixing Symbiotic Nodule Cells in Medicago truncatula and Other Nodulating Plants.

Root nodules formed by plants of the nitrogen-fixing clade (NFC) are symbiotic organs whose function is the maintenance and metabolic integration of large populations of nitrogen-fixing bacteria. These organs feature unique characteristics and processes, including their tissue organization, the presence of specific infection structures called infection threads, endocytotic uptake of bacteria, symbiotic cells that carry thousands of intracellular bacteria without signs of immune response, and the integration of symbiont and host metabolism. The early stages of the nodulation process are governed by a small set of well-defined functions, which together constitute the common symbiosis signaling pathway (CSSP). The CSSP activates a set of transcription factors (TFs) that orchestrate nodule organogenesis and infection. The later stages of nodule development require the activation of hundreds to thousands of genes, mostly expressed in the symbiotic cells. Many of these symbiotic cell-expressed genes are only active in these cells, reflecting the uniqueness of nodules as plant structures. While it is at present poorly understood how the nodule-specific transcriptome is activated and connected to early CSSP-signaling, candidate TFs have been identified by transcriptome approaches and the importance of epigenetic and chromatin-based regulation has been demonstrated. We further discuss how gene regulation analyses have advanced our understanding of nodule organogenesis and functioning of the symbiotic cells as well as the evolution of symbiosis in the NFC.